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gmx-distance(1)


NAME

   gmx-distance - Calculate distances between pairs of positions

SYNOPSIS

      gmx distance [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                   [-oav [<.xvg>]] [-oall [<.xvg>]] [-oxyz [<.xvg>]]
                   [-oh [<.xvg>]] [-oallstat [<.xvg>]] [-b <time>]
                   [-e <time>] [-dt <time>] [-tu <enum>]
                   [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc]
                   [-[no]pbc] [-sf <file>] [-selrpos <enum>]
                   [-seltype <enum>] [-select <selection>] [-len <real>]
                   [-tol <real>] [-binw <real>]

DESCRIPTION

   gmx  distance  calculates  distances  between  pairs  of positions as a
   function of time.  Each  selection  specifies  an  independent  set  of
   distances  to  calculate.  Each  selection  should  consist of pairs of
   positions, and the distances are computed between positions  1-2,  3-4,
   etc.

   -oav  writes  the  average  distance  as  a  function  of time for each
   selection.  -oall writes all the individual distances.  -oxyz does  the
   same,  but  the  x,  y,  and  z  components of the distance are written
   instead of the norm.  -oh writes a histogram of the distances for  each
   selection.   The  location  of the histogram is set with -len and -tol.
   Bin width is set with -binw.  -oallstat  writes  out  the  average  and
   standard  deviation  for  each individual distance, calculated over the
   frames.

   Note that gmx distance calculates distances between fixed  pairs  (1-2,
   3-4,  etc.)  within a single selection.  To calculate distances between
   two selections, including minimum, maximum, and pairwise distances, use
   gmx pairdist.

OPTIONS

   Options to specify input files:

   -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
          Input  trajectory  or  single configuration: xtc trr cpt gro g96
          pdb tng

   -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
          Input structure: tpr gro g96 pdb brk ent

   -n [<.ndx>] (index.ndx) (Optional)
          Extra index groups

   Options to specify output files:

   -oav [<.xvg>] (distave.xvg) (Optional)
          Average distances as function of time

   -oall [<.xvg>] (dist.xvg) (Optional)
          All distances as function of time

   -oxyz [<.xvg>] (distxyz.xvg) (Optional)
          Distance components as function of time

   -oh [<.xvg>] (disthist.xvg) (Optional)
          Histogram of the distances

   -oallstat [<.xvg>] (diststat.xvg) (Optional)
          Statistics for individual distances

   Other options:

   -b <time> (0)
          First frame (ps) to read from trajectory

   -e <time> (0)
          Last frame (ps) to read from trajectory

   -dt <time> (0)
          Only use frame if t MOD dt == first time (ps)

   -tu <enum> (ps)
          Unit for time values: fs, ps, ns, us, ms, s

   -fgroup <selection>
          Atoms stored in the trajectory file (if not set, assume first  N
          atoms)

   -xvg <enum> (xmgrace)
          Plot formatting: none, xmgrace, xmgr

   -[no]rmpbc (yes)
          Make molecules whole for each frame

   -[no]pbc (yes)
          Use periodic boundary conditions for distance calculation

   -sf <file>
          Provide selections from files

   -selrpos <enum> (atom)
          Selection  reference positions: atom, res_com, res_cog, mol_com,
          mol_cog,    whole_res_com,     whole_res_cog,     whole_mol_com,
          whole_mol_cog,    part_res_com,    part_res_cog,   part_mol_com,
          part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

   -seltype <enum> (atom)
          Default selection  output  positions:  atom,  res_com,  res_cog,
          mol_com,  mol_cog,  whole_res_com, whole_res_cog, whole_mol_com,
          whole_mol_cog,   part_res_com,    part_res_cog,    part_mol_com,
          part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

   -select <selection>
          Position pairs to calculate distances for

   -len <real> (0.1)
          Mean distance for histogramming

   -tol <real> (1)
          Width of full distribution as fraction of -len

   -binw <real> (0.001)
          Bin width for histogramming

SEE ALSO

   gmx(1)

   More     information    about    GROMACS    is    available    at    <
   http://www.gromacs.org/>.

COPYRIGHT

   2016, GROMACS development team



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